This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. We present a method for accurately estimating false discovery rates (FDR) in shotgun proteomics data sets by using a decoy database. This project involves first applying established statistical techniques for FDR estimation.